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Sodium in PDB 7z6j: X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl

Enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl

All present enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl, PDB code: 7z6j was solved by D.Loreto, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.31 / 1.53
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.61, 78.61, 37.41, 90, 90, 90
R / Rfree (%) 19.5 / 24.9

Other elements in 7z6j:

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl also contains other interesting chemical elements:

Rhodium (Rh) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl (pdb code 7z6j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl, PDB code: 7z6j:

Sodium binding site 1 out of 1 in 7z6j

Go back to Sodium Binding Sites List in 7z6j
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:28.9
occ:1.00
 HG A:SER72 2.0 32.0 0.0
O A:SER60 2.2 25.9 1.0
O A:HOH397 2.3 29.7 1.0
OG A:SER72 2.4 32.1 1.0
O A:ARG73 2.4 33.5 1.0
O A:CYS64 2.5 22.4 1.0
O A:HOH370 2.5 22.7 1.0
HB2 A:SER72 3.0 31.7 1.0
HA A:ASN65 3.1 22.1 1.0
CB A:SER72 3.2 30.7 1.0
C A:SER60 3.4 23.9 1.0
C A:ARG73 3.5 32.0 1.0
C A:CYS64 3.5 21.5 1.0
HB2 A:SER60 3.6 20.2 1.0
HA A:SER60 3.8 21.5 1.0
HB A:THR69 3.8 22.6 1.0
HB3 A:SER72 3.9 31.7 1.0
H A:CYS64 4.0 22.0 1.0
CA A:ASN65 4.0 23.0 1.0
H A:ASP66 4.0 19.6 1.0
HB2 A:ASN74 4.0 26.8 1.0
CA A:SER60 4.0 21.1 1.0
N A:ARG73 4.0 31.3 1.0
HA A:ASN74 4.1 27.1 1.0
C A:SER72 4.1 34.8 1.0
H A:ARG73 4.2 32.3 1.0
N A:ASN65 4.2 21.5 1.0
CA A:SER72 4.3 33.7 1.0
CB A:SER60 4.3 20.4 1.0
N A:ASN74 4.4 29.2 1.0
O A:ARG61 4.4 29.4 1.0
CA A:ARG73 4.4 32.2 1.0
HA A:ARG61 4.4 29.4 1.0
C A:ARG61 4.4 29.5 1.0
N A:ARG61 4.4 25.6 1.0
N A:CYS64 4.5 21.3 1.0
CA A:ASN74 4.6 26.6 1.0
OD1 A:ASN65 4.6 29.0 1.0
O A:HOH399 4.7 32.4 1.0
O A:SER72 4.7 33.1 1.0
CA A:CYS64 4.7 22.8 1.0
CA A:ARG61 4.7 29.8 1.0
CB A:THR69 4.7 23.5 1.0
N A:ASP66 4.7 19.9 1.0
HB2 A:ASN65 4.7 23.8 1.0
H A:TRP63 4.8 23.0 1.0
CB A:ASN74 4.8 26.6 1.0
HA A:ARG73 4.8 33.1 1.0
N A:TRP62 4.8 25.8 1.0
HG22 A:THR69 4.8 23.3 1.0
HG1 A:THR69 4.8 20.0 0.0
C A:ASN65 4.9 19.3 1.0
CB A:ASN65 4.9 23.5 1.0
HA A:SER72 4.9 32.9 1.0
O A:THR69 4.9 23.5 1.0
H A:TRP62 5.0 26.8 1.0

Reference:

D.Loreto, A.Esposito, N.Demitri, A.Guaragna, A.Merlino. Reactivity of A Fluorine-Containing Dirhodium Tetracarboxylate Compound with Proteins To Be Published.
Page generated: Mon Aug 18 12:45:37 2025

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